Loading Library

library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)

Loading the expressions and pathway sets of Leukemia databse

We use the colapsed symbols to genes expression data for expressions. GSEA uses a chip functoin for connecting the uncollapsed to collapsed data. I am currently figuring out how ti perfprms that step. For now not collapsing serves the purpose. Genotypes are 33 mutants and 17 wild types. Pathways are read as done is GSEA. To remain consistent with GSEA we remove the pathways with sizes below 15 and above 500 as well as pathways that have less than 15 genes present in inside the expression matrix.

expressions <- read.csv("./GSEA leukemia/Leukemia_collapsed_symbols_for_R.csv", sep = ",", row.names = 1)
genotypes <- read.csv("./GSEA leukemia/Leukemia_genotype.txt", sep=" ", header = F)
genotypes <- as.vector(unname(ifelse( genotypes=="ALL",1,0)))
gene_names <- rownames(expressions)
expressions <- expressions[-1]
expressions <- t(expressions)
dim(expressions)
## [1]    48 10056
# pathway <- read.csv("./msigdb_v6.2_files_to_download_locally/msigdb_v6.2_GMTs_R/positional gene sets/c1.all.v6.2.symbols.csv", sep = ",", row.names = 1,na.strings = "", colClasses="character")

pathway <- read.csv("./msigdb_v6.2_files_to_download_locally/msigdb_v6.2_GMTs_R/curated gene sets/c2.all.v6.2.symbols.csv", sep = ",", row.names = 1,na.strings = "", colClasses="character")
pathway <- pathway[,-1]
pathway <- t(pathway)
row.names(pathway) <- NULL
pathway <- as.data.frame(pathway)
pathway=lapply(pathway, function(x) x[!is.na(x)] )
pathway=lapply(pathway, function(x) as.character(x))
pathway_collapsed <- pathway[sapply(pathway,function(x) {(15 <= length(x)) &&(length(x) <= 500)&& sum(colnames(expressions)%in%x)>15})]
min(sapply(pathway_collapsed,length))
## [1] 16
individual_pathway_length <- sapply(pathway_collapsed,length)
gene_number <- length(gene_names)
pathway_number <- length(individual_pathway_length)

Loading the results of running GSEA on Leukemia dataset

GSEA was separately run and the enrichment results are saved. We upload the results and select the significant findings.

gsea_results <- read.csv("./GSEA leukemia/gsea_leukimia_enrichment_results6.2_curated.csv", sep = ",", row.names = 1)
# rownames(gsea_results) <- tolower(rownames(gsea_results))
gsea_results_significant <- subset(gsea_results, NOM.p.val <0.05 )

Running Dcor and Univariate ttest over the pathways

Expressions concordant with specific pathways are chosen and dcor and univariate t.test are applied on them. The univariate test is adjusted for FDR correction.

dcor_results <- list()
univariate_results <- list()
univariate_results_adjusted <- list()

for (ii in 1:length(pathway_collapsed)){
pathway_expressions <- expressions[,colnames(expressions)%in% pathway_collapsed[[ii]]]

 dcor_results[ii] <- dcor((pathway_expressions),(genotypes))

}
names(dcor_results)  <- names( pathway_collapsed)

Simulating MPEA Surrogate over the array.

set.seed(0)
# surrogate_dcor <- list()
num_simulation <- 999
cl<-makeCluster(6)
registerDoParallel(cl)

surrogate_dcor <- foreach (ii = 1:pathway_number,  .export = c("num_simulation","gene_number","individual_pathway_length","genotypes"), .packages = "energy") %dopar%{
  if(ii%%100==0) print(ii)
  aux_dcor <- NULL
    for ( jj in 1: num_simulation)
    {
      aux_genes <- sample(1:gene_number,individual_pathway_length[ii])
      aux_dcor[jj] <- dcor(expressions[,aux_genes],genotypes)
    
    }  
  # surrogate_dcor[[ii]] <- aux_dcor
  aux_dcor
}
## Warning in e$fun(obj, substitute(ex), parent.frame(), e$data):
## already exporting variable(s): num_simulation, gene_number,
## individual_pathway_length, genotypes
stopCluster(cl)
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (1+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
##                        AIGNER_ZEB1_TARGETS 
##                                      0.001 
##             HADDAD_B_LYMPHOCYTE_PROGENITOR 
##                                      0.001 
##      SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 
##                                      0.001 
##          ROME_INSULIN_TARGETS_IN_MUSCLE_DN 
##                                      0.001 
##            POOLA_INVASIVE_BREAST_CANCER_UP 
##                                      0.001 
##             YAGI_AML_WITH_11Q23_REARRANGED 
##                                      0.001 
##                     DELACROIX_RAR_BOUND_ES 
##                                      0.001 
##                         RAO_BOUND_BY_SALL4 
##                                      0.001 
## REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS 
##                                      0.002 
##   SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 
##                                      0.002
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
nominal_dcor_q_values_under_25
## named numeric(0)

Identifying the pathways deemed significant in both GSEA and MPEA

Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))

Mutually_identified_in_GSEA_dcor
##  [1] "HADDAD_B_LYMPHOCYTE_PROGENITOR"                                                       
##  [2] "RAO_BOUND_BY_SALL4"                                                                   
##  [3] "BORCZUK_MALIGNANT_MESOTHELIOMA_DN"                                                    
##  [4] "GOLUB_ALL_VS_AML_UP"                                                                  
##  [5] "HUMMEL_BURKITTS_LYMPHOMA_UP"                                                          
##  [6] "KLEIN_TARGETS_OF_BCR_ABL1_FUSION"                                                     
##  [7] "PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN"                                                  
##  [8] "REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS"
##  [9] "REACTOME_GPCR_LIGAND_BINDING"                                                         
## [10] "KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN"                                                   
## [11] "VALK_AML_CLUSTER_1"                                                                   
## [12] "BIOCARTA_CTCF_PATHWAY"                                                                
## [13] "KEGG_PRIMARY_IMMUNODEFICIENCY"                                                        
## [14] "SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES"                                                  
## [15] "HOLLMANN_APOPTOSIS_VIA_CD40_DN"                                                       
## [16] "WANG_CLIM2_TARGETS_DN"                                                                
## [17] "PROVENZANI_METASTASIS_UP"                                                             
## [18] "BROWN_MYELOID_CELL_DEVELOPMENT_UP"                                                    
## [19] "HOSHIDA_LIVER_CANCER_SURVIVAL_UP"                                                     
## [20] "BAELDE_DIABETIC_NEPHROPATHY_DN"                                                       
## [21] "SESTO_RESPONSE_TO_UV_C5"                                                              
## [22] "SIG_BCR_SIGNALING_PATHWAY"                                                            
## [23] "RIZKI_TUMOR_INVASIVENESS_2D_UP"                                                       
## [24] "REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR"                                        
## [25] "BHAT_ESR1_TARGETS_VIA_AKT1_DN"                                                        
## [26] "BASSO_CD40_SIGNALING_DN"                                                              
## [27] "PARK_HSC_AND_MULTIPOTENT_PROGENITORS"                                                 
## [28] "LEE_RECENT_THYMIC_EMIGRANT"                                                           
## [29] "LABBE_WNT3A_TARGETS_UP"                                                               
## [30] "CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE"                                               
## [31] "HAMAI_APOPTOSIS_VIA_TRAIL_DN"                                                         
## [32] "BILANGES_SERUM_SENSITIVE_VIA_TSC2"                                                    
## [33] "NOUZOVA_TRETINOIN_AND_H4_ACETYLATION"                                                 
## [34] "LEE_LIVER_CANCER_E2F1_UP"                                                             
## [35] "BOYLAN_MULTIPLE_MYELOMA_PCA3_DN"                                                      
## [36] "ZHAN_MULTIPLE_MYELOMA_PR_DN"                                                          
## [37] "BAKKER_FOXO3_TARGETS_DN"                                                              
## [38] "CROMER_METASTASIS_UP"                                                                 
## [39] "REACTOME_PI_METABOLISM"                                                               
## [40] "ST_B_CELL_ANTIGEN_RECEPTOR"                                                           
## [41] "PID_BCR_5PATHWAY"                                                                     
## [42] "PID_BETA_CATENIN_NUC_PATHWAY"                                                         
## [43] "CHESLER_BRAIN_QTL_CIS"

Identifying the pathways significant in MPEA not in GSEA

Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
AIGNER_ZEB1_TARGETS SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 ROME_INSULIN_TARGETS_IN_MUSCLE_DN POOLA_INVASIVE_BREAST_CANCER_UP YAGI_AML_WITH_11Q23_REARRANGED DELACROIX_RAR_BOUND_ES REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP JI_METASTASIS_REPRESSED_BY_STK11 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN HOELZEL_NF1_TARGETS_DN DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN PASINI_SUZ12_TARGETS_UP REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS ROY_WOUND_BLOOD_VESSEL_DN IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM TSENG_ADIPOGENIC_POTENTIAL_UP SMID_BREAST_CANCER_NORMAL_LIKE_UP AMIT_SERUM_RESPONSE_480_MCF10A MAHADEVAN_IMATINIB_RESISTANCE_DN INGRAM_SHH_TARGETS_DN RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP DAWSON_METHYLATED_IN_LYMPHOMA_TCL1 KUMAR_TARGETS_OF_MLL_AF9_FUSION DE_YY1_TARGETS_DN COATES_MACROPHAGE_M1_VS_M2_DN XU_GH1_AUTOCRINE_TARGETS_UP CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY BURTON_ADIPOGENESIS_11 LABBE_WNT3A_TARGETS_DN VANTVEER_BREAST_CANCER_BRCA1_UP FERRANDO_HOX11_NEIGHBORS SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP PENG_RAPAMYCIN_RESPONSE_UP BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING GRADE_COLON_VS_RECTAL_CANCER_DN REACTOME_G_ALPHA_I_SIGNALLING_EVENTS REACTOME_L1CAM_INTERACTIONS JAEGER_METASTASIS_UP SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY ZHAN_MULTIPLE_MYELOMA_CD2_UP KAMMINGA_SENESCENCE MANN_RESPONSE_TO_AMIFOSTINE_UP PETRETTO_CARDIAC_HYPERTROPHY SANSOM_APC_TARGETS_DN HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN RIGGI_EWING_SARCOMA_PROGENITOR_DN BAUS_TFF2_TARGETS_UP MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN HECKER_IFNB1_TARGETS LIU_SOX4_TARGETS_UP BOCHKIS_FOXA2_TARGETS SIMBULAN_PARP1_TARGETS_DN ONO_FOXP3_TARGETS_DN HOLLERN_EMT_BREAST_TUMOR_DN WONG_IFNA2_RESISTANCE_DN GRESHOCK_CANCER_COPY_NUMBER_UP MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN ONO_AML1_TARGETS_DN CHANG_IMMORTALIZED_BY_HPV31_UP FUJII_YBX1_TARGETS_DN SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN DELLA_RESPONSE_TO_TSA_AND_BUTYRATE BURTON_ADIPOGENESIS_7 BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 YANG_BREAST_CANCER_ESR1_LASER_DN XU_CREBBP_TARGETS_DN WOO_LIVER_CANCER_RECURRENCE_UP BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN VERHAAK_AML_WITH_NPM1_MUTATED_DN PLASARI_TGFB1_TARGETS_10HR_DN DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP QI_PLASMACYTOMA_UP SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 WIELAND_UP_BY_HBV_INFECTION LIU_VAV3_PROSTATE_CARCINOGENESIS_UP REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE REACTOME_REGULATION_OF_SIGNALING_BY_CBL VECCHI_GASTRIC_CANCER_EARLY_DN BROWNE_HCMV_INFECTION_48HR_UP RIZKI_TUMOR_INVASIVENESS_3D_UP ISSAEVA_MLL2_TARGETS JOHNSTONE_PARVB_TARGETS_3_UP YAMAZAKI_TCEB3_TARGETS_DN ZHU_CMV_24_HR_DN ZHENG_FOXP3_TARGETS_IN_THYMUS_UP HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP GAVIN_FOXP3_TARGETS_CLUSTER_P2 REACTOME_NEPHRIN_INTERACTIONS SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP AMIT_SERUM_RESPONSE_240_MCF10A NUTT_GBM_VS_AO_GLIOMA_UP MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 ALFANO_MYC_TARGETS EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP MARSON_FOXP3_TARGETS_STIMULATED_UP LU_TUMOR_ANGIOGENESIS_UP VERHAAK_GLIOBLASTOMA_PRONEURAL CHENG_RESPONSE_TO_NICKEL_ACETATE ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP REACTOME_MYOGENESIS MORI_LARGE_PRE_BII_LYMPHOCYTE_DN BECKER_TAMOXIFEN_RESISTANCE_DN CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN KEGG_PROTEASOME NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN REACTOME_DEVELOPMENTAL_BIOLOGY ONDER_CDH1_TARGETS_2_UP VALK_AML_CLUSTER_15 ZHAN_MULTIPLE_MYELOMA_HP_DN BIOCARTA_PROTEASOME_PATHWAY WNT_SIGNALING REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN STONER_ESOPHAGEAL_CARCINOGENESIS_UP TAVAZOIE_METASTASIS DANG_MYC_TARGETS_DN JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP LIAO_HAVE_SOX4_BINDING_SITES LEE_LIVER_CANCER_DENA_UP KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN LEE_LIVER_CANCER_ACOX1_UP CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION ULE_SPLICING_VIA_NOVA2
MPEA 0.0010 0.0010 0.0010 0.0010 0.0010 0.0010 0.0020 0.0020 0.002 0.0030 0.0030 0.0030 0.0030 0.0040 0.0040 0.0040 0.0040 0.0040 0.0060 0.0070 0.0070 0.0070 0.0080 0.0080 0.0080 0.0080 0.009 0.010 0.0100 0.0110 0.0110 0.0110 0.0110 0.0120 0.0120 0.0130 0.0130 0.0140 0.0140 0.0140 0.0140 0.014 0.0140 0.0150 0.0150 0.0150 0.0150 0.0160 0.0160 0.016 0.0180 0.0180 0.0190 0.0190 0.0200 0.0200 0.0200 0.021 0.0210 0.0220 0.022 0.0240 0.0240 0.0250 0.0260 0.0260 0.0260 0.0260 0.0260 0.0260 0.0260 0.0270 0.0270 0.0270 0.0280 0.0290 0.030 0.0310 0.0310 0.0320 0.032 0.0330 0.0330 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0350 0.0360 0.0360 0.0360 0.0360 0.0370 0.0370 0.038 0.0380 0.0380 0.0390 0.0390 0.0390 0.039 0.0400 0.0400 0.0400 0.0400 0.0410 0.041 0.0420 0.0420 0.0420 0.0420 0.0430 0.0430 0.044 0.0440 0.0440 0.0440 0.0450 0.0450 0.0450 0.045 0.0450 0.0450 0.0450 0.047 0.0470 0.0470 0.0470 0.0480 0.0480 0.0480 0.0490 0.0490
GSEA 0.4809 0.5105 0.3888 0.4875 0.0702 0.1395 0.0682 0.8162 0.192 0.5824 0.3519 0.1916 0.0672 0.0564 0.5845 0.0529 0.3188 0.1841 0.1279 0.3295 0.2769 0.7079 0.3265 0.3961 0.1954 0.2147 0.300 0.298 0.0691 0.0651 0.5168 0.1065 0.0564 0.9006 0.1085 0.7449 0.5645 0.1561 0.6263 0.3683 0.6918 0.217 0.1755 0.5238 0.7196 0.1734 0.2031 0.5068 0.6667 0.081 0.4853 0.6047 0.0602 0.3613 0.3727 0.2275 0.9075 0.284 0.0885 0.3168 0.072 0.5835 0.1085 0.3451 0.1042 0.1303 0.1731 0.3477 0.1896 0.2344 0.1727 0.1837 0.2589 0.4962 0.5156 0.1695 0.524 0.4118 0.1319 0.1708 0.264 0.1453 0.4482 0.0861 0.4766 0.4693 0.2675 0.2994 0.4442 0.1159 0.1111 0.1957 0.0606 0.4462 0.1184 0.2308 0.072 0.7152 0.2643 0.2879 0.1238 0.2605 0.578 0.5869 0.8472 0.2337 0.5312 0.4347 0.176 0.2089 0.5494 0.6851 0.6854 0.0664 0.0668 0.739 0.8323 0.4981 0.1946 0.1205 0.4738 0.0916 0.753 0.1761 0.9189 0.2945 0.483 0.2927 0.1016 0.7425 0.5703 0.2838 0.5545 0.7992 0.9552

Identifying the pathways significant in GSEA not in MPEA

Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN PUJANA_BRCA2_PCC_NETWORK KEGG_BASE_EXCISION_REPAIR REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES REACTOME_CELL_CYCLE GARY_CD5_TARGETS_DN MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6 DAZARD_RESPONSE_TO_UV_NHEK_DN BENPORATH_PROLIFERATION NA KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP RAMALHO_STEMNESS_UP DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER REACTOME_CELL_CYCLE_CHECKPOINTS REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION GENTILE_UV_RESPONSE_CLUSTER_D8 MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP REACTOME_HIV_LIFE_CYCLE NA REACTOME_HIV_INFECTION REACTOME_CHROMOSOME_MAINTENANCE FIGUEROA_AML_METHYLATION_CLUSTER_1_DN ZHANG_BREAST_CANCER_PROGENITORS_UP PYEON_HPV_POSITIVE_TUMORS_UP MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP NA SHEN_SMARCA2_TARGETS_UP GRADE_METASTASIS_DN NA REACTOME_BASE_EXCISION_REPAIR REACTOME_CELL_CYCLE_MITOTIC REACTOME_TRANSCRIPTION KAUFFMANN_DNA_REPAIR_GENES ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP MITSIADES_RESPONSE_TO_APLIDIN_DN REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS BOYLAN_MULTIPLE_MYELOMA_C_D_UP NA REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY REACTOME_TELOMERE_MAINTENANCE BIDUS_METASTASIS_UP ZHANG_TLX_TARGETS_36HR_DN MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL KIM_WT1_TARGETS_DN MORI_PLASMA_CELL_DN ENK_UV_RESPONSE_KERATINOCYTE_DN ZHAN_EARLY_DIFFERENTIATION_GENES_DN REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP MATTIOLI_MGUS_VS_PCL ABRAMSON_INTERACT_WITH_AIRE ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP VILLANUEVA_LIVER_CANCER_KRT19_UP REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE KEGG_SPLICEOSOME MORI_MATURE_B_LYMPHOCYTE_DN DITTMER_PTHLH_TARGETS_DN CAIRO_HEPATOBLASTOMA_UP BIOCARTA_BCR_PATHWAY REACTOME_MRNA_PROCESSING NA ROSS_AML_WITH_AML1_ETO_FUSION REACTOME_GLUCOSE_TRANSPORT REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE PECE_MAMMARY_STEM_CELL_DN DAZARD_UV_RESPONSE_CLUSTER_G6 GENTILE_UV_RESPONSE_CLUSTER_D4 REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE KAMMINGA_EZH2_TARGETS NA HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2 BROWNE_HCMV_INFECTION_10HR_DN PEART_HDAC_PROLIFERATION_CLUSTER_UP PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE GALE_APL_WITH_FLT3_MUTATED_UP REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC BIOCARTA_CARM_ER_PATHWAY REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION VALK_AML_CLUSTER_10 NA NA BIOCARTA_PAR1_PATHWAY SESTO_RESPONSE_TO_UV_C2 CARD_MIR302A_TARGETS REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1 REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION ELLWOOD_MYC_TARGETS_DN NA KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS BROWNE_HCMV_INFECTION_4HR_DN PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP WAKASUGI_HAVE_ZNF143_BINDING_SITES NA ROESSLER_LIVER_CANCER_METASTASIS_DN REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION BENPORATH_ES_1 PID_EPHA2_FWD_PATHWAY REACTOME_RNA_POL_I_TRANSCRIPTION YANG_BREAST_CANCER_ESR1_DN REACTOME_MEIOSIS REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC BOYLAN_MULTIPLE_MYELOMA_C_UP KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT HOLLMANN_APOPTOSIS_VIA_CD40_UP WHITFIELD_CELL_CYCLE_G2_M BRUINS_UVC_RESPONSE_MIDDLE PID_P38_MK2_PATHWAY KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP CHENG_IMPRINTED_BY_ESTRADIOL NA RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP TIEN_INTESTINE_PROBIOTICS_2HR_DN ZUCCHI_METASTASIS_UP PID_P53_REGULATION_PATHWAY BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS KIM_GERMINAL_CENTER_T_HELPER_UP PID_PS1_PATHWAY OUILLETTE_CLL_13Q14_DELETION_UP THUM_SYSTOLIC_HEART_FAILURE_DN REACTOME_APOPTOSIS PID_AR_NONGENOMIC_PATHWAY ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP JI_RESPONSE_TO_FSH_UP BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP SIG_CHEMOTAXIS BRUINS_UVC_RESPONSE_EARLY_LATE LIN_MELANOMA_COPY_NUMBER_DN NA JOHNSTONE_PARVB_TARGETS_2_DN NA KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP LAIHO_COLORECTAL_CANCER_SERRATED_DN PID_HEDGEHOG_GLI_PATHWAY LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q LIN_MELANOMA_COPY_NUMBER_UP DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP BIOCARTA_TFF_PATHWAY HOSHIDA_LIVER_CANCER_SUBCLASS_S2 BENPORATH_OCT4_TARGETS GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP NA SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP NA KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN BILD_E2F3_ONCOGENIC_SIGNATURE NA WOOD_EBV_EBNA1_TARGETS_DN NA WINTER_HYPOXIA_DN IKEDA_MIR30_TARGETS_UP REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD HASLINGER_B_CLL_WITH_6Q21_DELETION BIOCARTA_WNT_PATHWAY YAGI_AML_WITH_T_9_11_TRANSLOCATION HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN BIOCARTA_CXCR4_PATHWAY TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN ZHAN_MULTIPLE_MYELOMA_HP_UP REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP NA BILBAN_B_CLL_LPL_UP CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS KEGG_NOTCH_SIGNALING_PATHWAY HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP LEE_CALORIE_RESTRICTION_MUSCLE_DN KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS KATSANOU_ELAVL1_TARGETS_DN GYORFFY_MITOXANTRONE_RESISTANCE MULLIGHAN_NPM1_SIGNATURE_3_DN JIANG_TIP30_TARGETS_UP REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 HOFMANN_CELL_LYMPHOMA_UP STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP ABBUD_LIF_SIGNALING_1_UP DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS CHEOK_RESPONSE_TO_HD_MTX_UP REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS VERHAAK_AML_WITH_NPM1_MUTATED_UP PID_INTEGRIN_CS_PATHWAY PID_UPA_UPAR_PATHWAY REACTOME_COLLAGEN_FORMATION DALESSIO_TSA_RESPONSE GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 BIOCARTA_DC_PATHWAY NAKAJIMA_MAST_CELL REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE KIM_ALL_DISORDERS_CALB1_CORR_DN GOLUB_ALL_VS_AML_DN PID_INTEGRIN2_PATHWAY HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS KRIEG_HYPOXIA_VIA_KDM3A PID_SYNDECAN_1_PATHWAY PARK_APL_PATHOGENESIS_DN HWANG_PROSTATE_CANCER_MARKERS NA AMIT_EGF_RESPONSE_120_MCF10A LI_CISPLATIN_RESISTANCE_DN REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL VERRECCHIA_RESPONSE_TO_TGFB1_C2 GROSS_ELK3_TARGETS_DN ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION NABA_COLLAGENS GHANDHI_BYSTANDER_IRRADIATION_UP KOHOUTEK_CCNT1_TARGETS TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN KOBAYASHI_EGFR_SIGNALING_6HR_DN REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP KEGG_ARACHIDONIC_ACID_METABOLISM NA ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP HOLLERN_MICROACINAR_BREAST_TUMOR_UP WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN MIKKELSEN_MEF_ICP_WITH_H3K27ME3 GHANDHI_DIRECT_IRRADIATION_UP BIOCARTA_CYTOKINE_PATHWAY MIKKELSEN_MEF_LCP_WITH_H3K27ME3 YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP VERRECCHIA_RESPONSE_TO_TGFB1_C1 PID_RXR_VDR_PATHWAY XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES HUPER_BREAST_BASAL_VS_LUMINAL_UP NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN JEON_SMAD6_TARGETS_UP PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP PID_INTEGRIN5_PATHWAY NA NAKAMURA_ADIPOGENESIS_EARLY_UP BIOCARTA_INFLAM_PATHWAY BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS KHETCHOUMIAN_TRIM24_TARGETS_UP NAKAJIMA_EOSINOPHIL SEMENZA_HIF1_TARGETS MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP AMIT_EGF_RESPONSE_120_HELA NA FIGUEROA_AML_METHYLATION_CLUSTER_5_DN REACTOME_AMINE_LIGAND_BINDING_RECEPTORS SABATES_COLORECTAL_ADENOMA_UP PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A MADAN_DPPA4_TARGETS URS_ADIPOCYTE_DIFFERENTIATION_UP ONDER_CDH1_SIGNALING_VIA_CTNNB1 KERLEY_RESPONSE_TO_CISPLATIN_UP CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN MARKEY_RB1_CHRONIC_LOF_DN SHEN_SMARCA2_TARGETS_DN NABA_ECM_AFFILIATED KIM_LIVER_CANCER_POOR_SURVIVAL_DN REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS NA WATANABE_COLON_CANCER_MSI_VS_MSS_UP MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP
MPEA 0.050 0.3470 0.2320 0.1090 0.12 0.5520 0.2540 0.585 0.0840 0.4770 0.3420 NA 0.072 0.5320 0.509 0.5880 0.4030 0.1660 0.2510 0.1000 0.2270 0.2250 NA 0.1860 0.2620 0.6410 0.4470 0.2140 0.6180 0.181 NA 0.794 0.058 NA 0.2290 0.3840 0.8390 0.1510 0.0710 0.1630 0.4250 0.5630 0.3500 0.6360 NA 0.3850 0.1990 0.8580 0.6180 0.3370 0.3430 0.3780 0.467 0.2970 0.1340 0.1130 0.971 0.1750 0.1480 0.441 0.8450 0.7590 0.6480 0.2680 0.5440 0.0920 0.0640 0.7820 NA 0.2480 0.6380 0.120 0.6350 0.0610 0.3220 0.3010 0.8120 0.1200 0.0780 NA 0.2330 0.3950 0.2070 0.0930 0.1060 0.1470 0.1040 0.2610 0.0750 0.2300 0.3190 0.0760 NA NA 0.2440 0.2650 0.373 0.0910 0.0880 0.7830 0.8090 NA 0.2750 0.8380 0.8540 0.4500 NA 0.7940 0.4810 0.0840 0.872 0.2940 0.9570 0.708 0.9430 0.4530 0.0700 0.1980 0.8380 0.6620 0.8080 0.452 0.2120 0.4160 0.8100 NA 0.2270 0.3340 0.4440 0.7380 0.376 0.5720 0.7980 0.5780 0.4590 0.7000 0.0880 0.9020 0.795 0.166 0.6660 0.0960 0.6870 0.6730 NA 0.1430 NA 0.0880 0.512 0.3450 0.9110 0.2530 0.3530 0.2300 0.8370 0.4480 0.7330 0.1680 NA 0.4860 NA 0.3520 0.7680 NA 0.0890 NA 0.0590 0.1770 0.1010 0.2920 0.8030 0.0840 0.2730 0.5320 0.0820 0.6680 0.9720 0.1630 0.4890 0.7610 0.1140 0.238 NA 0.6730 0.7410 0.6740 0.2790 0.1420 0.0640 0.8500 0.0770 0.8600 0.2650 0.107 0.1680 0.3350 0.9250 0.3140 0.4780 0.448 0.4090 0.3340 0.675 0.4970 0.1520 0.313 0.84 0.1390 0.0660 0.2220 0.2290 0.0600 0.7070 0.6710 0.089 0.0520 0.5200 0.3800 0.9620 0.1540 0.2700 0.0690 NA 0.8130 0.745 0.3620 0.3070 0.744 0.8270 0.7770 0.678 0.4880 0.3210 0.832 0.7100 0.9990 0.6330 0.9920 0.0960 0.6250 NA 0.743 0.3820 0.1600 0.0970 0.9990 0.8290 0.4450 0.9480 0.4190 0.1340 0.5560 0.1910 0.4930 0.6820 0.9820 0.8510 0.3280 0.9270 0.2810 NA 0.8070 0.4290 0.9760 0.2380 0.289 0.2530 0.6670 0.6470 0.4180 NA 0.4470 0.9350 0.9720 0.1850 0.5870 0.9050 0.5410 0.6000 0.0690 0.1500 1.0000 0.9670 0.3630 0.3990 0.9720 0.4500 0.1790 0.9020 NA 0.947 0.6590
GSEA 0.006 0.0039 0.0081 0.0218 0.00 0.0079 0.0216 0.006 0.0157 0.0141 0.0426 0.022 0.002 0.0039 0.004 0.0139 0.0039 0.0194 0.0175 0.0041 0.0462 0.0182 0.0198 0.0158 0.0189 0.0077 0.0142 0.0197 0.0155 0.048 0.0347 0.020 0.018 0.0038 0.0039 0.0374 0.0059 0.0277 0.0041 0.0077 0.0062 0.0436 0.0199 0.0122 0.0335 0.0201 0.0189 0.0266 0.0283 0.0261 0.0161 0.0101 0.025 0.0451 0.0137 0.0294 0.002 0.0317 0.0385 0.006 0.0356 0.0242 0.0356 0.0472 0.0121 0.0061 0.0079 0.0455 0.0062 0.0059 0.0139 0.035 0.0245 0.0019 0.0402 0.0179 0.0258 0.0379 0.0472 0.0372 0.0277 0.0082 0.0292 0.0254 0.0409 0.0294 0.0371 0.0461 0.0329 0.0454 0.0296 0.0098 0.0126 0.0241 0.0102 0.0041 0.006 0.0352 0.0388 0.0214 0.0057 0.0081 0.0099 0.0061 0.0202 0.0258 0.0344 0.0198 0.0459 0.0464 0.032 0.0386 0.0085 0.041 0.0081 0.0298 0.0484 0.0205 0.0176 0.0266 0.0484 0.014 0.0292 0.0188 0.0102 0.0431 0.0359 0.0475 0.0371 0.0385 0.012 0.0466 0.0216 0.0141 0.0041 0.0141 0.0281 0.0271 0.000 0.014 0.0222 0.0021 0.0211 0.0348 0.0394 0.0346 0.0329 0.0198 0.045 0.0183 0.0423 0.0304 0.0202 0.0282 0.0377 0.0482 0.0103 0.0356 0.0426 0.0224 0.0266 0.0165 0.0285 0.0381 0.0217 0.0372 0.0316 0.0401 0.0311 0.0331 0.0375 0.0461 0.0319 0.0199 0.0402 0.0218 0.0275 0.0274 0.0338 0.0454 0.0276 0.039 0.0427 0.0476 0.0188 0.0411 0.0344 0.0381 0.0402 0.0481 0.0225 0.0406 0.0364 0.048 0.0447 0.0379 0.0355 0.0478 0.0473 0.000 0.0037 0.0019 0.000 0.0078 0.0059 0.000 0.00 0.0113 0.0096 0.0038 0.0038 0.0038 0.0019 0.0038 0.000 0.0079 0.0152 0.0056 0.0201 0.0019 0.0353 0.0113 0.0242 0.0119 0.018 0.0057 0.0133 0.019 0.0321 0.0077 0.028 0.0249 0.0059 0.015 0.0078 0.0254 0.0156 0.0169 0.0114 0.0186 0.0252 0.019 0.0152 0.0333 0.0296 0.0019 0.0411 0.0209 0.0152 0.0111 0.0189 0.0248 0.0273 0.0252 0.0189 0.0099 0.0135 0.0328 0.0496 0.0361 0.0418 0.0421 0.0397 0.0365 0.0376 0.035 0.0291 0.0474 0.0342 0.0336 0.0382 0.0301 0.0411 0.0416 0.0342 0.0483 0.0262 0.0337 0.0361 0.0216 0.0412 0.0157 0.0437 0.0366 0.0473 0.0391 0.0366 0.0476 0.0218 0.0371 0.049 0.0301

Univariate Significance analysis on single pathway gene by gene Significant in MPEA and not in GSEA

enrichment_ratio_dcor <- NULL
enrichment_ratio_ttest <- NULL
for ( ii in 1:length(Significant_in_dcor_not_in_GSEA) ){
aux_genes <- intersect(pathway_collapsed[[Significant_in_dcor_not_in_GSEA[[ii]]]],colnames(expressions))
aux_pathway_dcor <- dcor.test(dist(expressions[,aux_genes]),dist(genotypes),R=10000)
aux_individual_genes_in_pathway_dcor <- sapply(aux_genes,function(x) dcor.test(dist(expressions[,x]),dist(genotypes),R=10000)$p.value<0.05 )
aux_enrichment_ratio_dcor <- sum(aux_individual_genes_in_pathway_dcor)/length(aux_individual_genes_in_pathway_dcor)
enrichment_ratio_dcor[ii] <- aux_enrichment_ratio_dcor

aux_individual_genes_in_pathway_ttest <- sapply(aux_genes,function(x) t.test(expressions[,x]~genotypes)$p.value<0.05 )
aux_enrichment_ratio_ttest <- sum(aux_individual_genes_in_pathway_ttest)/length(aux_individual_genes_in_pathway_ttest)
aux_enrichment_ratio_ttest
enrichment_ratio_ttest[ii] <-aux_enrichment_ratio_ttest
}

enrichment_ratio_comparison <- rbind(enrichment_ratio_dcor,enrichment_ratio_ttest)
rownames(enrichment_ratio_comparison) <- c("MPEA","GSEA")
colnames(enrichment_ratio_comparison) <- Significant_in_dcor_not_in_GSEA

enrichment_ratio_comparison%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
AIGNER_ZEB1_TARGETS SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 ROME_INSULIN_TARGETS_IN_MUSCLE_DN POOLA_INVASIVE_BREAST_CANCER_UP YAGI_AML_WITH_11Q23_REARRANGED DELACROIX_RAR_BOUND_ES REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP JI_METASTASIS_REPRESSED_BY_STK11 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN HOELZEL_NF1_TARGETS_DN DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN PASINI_SUZ12_TARGETS_UP REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS ROY_WOUND_BLOOD_VESSEL_DN IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM TSENG_ADIPOGENIC_POTENTIAL_UP SMID_BREAST_CANCER_NORMAL_LIKE_UP AMIT_SERUM_RESPONSE_480_MCF10A MAHADEVAN_IMATINIB_RESISTANCE_DN INGRAM_SHH_TARGETS_DN RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP DAWSON_METHYLATED_IN_LYMPHOMA_TCL1 KUMAR_TARGETS_OF_MLL_AF9_FUSION DE_YY1_TARGETS_DN COATES_MACROPHAGE_M1_VS_M2_DN XU_GH1_AUTOCRINE_TARGETS_UP CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY BURTON_ADIPOGENESIS_11 LABBE_WNT3A_TARGETS_DN VANTVEER_BREAST_CANCER_BRCA1_UP FERRANDO_HOX11_NEIGHBORS SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP PENG_RAPAMYCIN_RESPONSE_UP BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING GRADE_COLON_VS_RECTAL_CANCER_DN REACTOME_G_ALPHA_I_SIGNALLING_EVENTS REACTOME_L1CAM_INTERACTIONS JAEGER_METASTASIS_UP SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY ZHAN_MULTIPLE_MYELOMA_CD2_UP KAMMINGA_SENESCENCE MANN_RESPONSE_TO_AMIFOSTINE_UP PETRETTO_CARDIAC_HYPERTROPHY SANSOM_APC_TARGETS_DN HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN RIGGI_EWING_SARCOMA_PROGENITOR_DN BAUS_TFF2_TARGETS_UP MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN HECKER_IFNB1_TARGETS LIU_SOX4_TARGETS_UP BOCHKIS_FOXA2_TARGETS SIMBULAN_PARP1_TARGETS_DN ONO_FOXP3_TARGETS_DN HOLLERN_EMT_BREAST_TUMOR_DN WONG_IFNA2_RESISTANCE_DN GRESHOCK_CANCER_COPY_NUMBER_UP MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN ONO_AML1_TARGETS_DN CHANG_IMMORTALIZED_BY_HPV31_UP FUJII_YBX1_TARGETS_DN SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN DELLA_RESPONSE_TO_TSA_AND_BUTYRATE BURTON_ADIPOGENESIS_7 BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 YANG_BREAST_CANCER_ESR1_LASER_DN XU_CREBBP_TARGETS_DN WOO_LIVER_CANCER_RECURRENCE_UP BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN VERHAAK_AML_WITH_NPM1_MUTATED_DN PLASARI_TGFB1_TARGETS_10HR_DN DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP QI_PLASMACYTOMA_UP SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 WIELAND_UP_BY_HBV_INFECTION LIU_VAV3_PROSTATE_CARCINOGENESIS_UP REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE REACTOME_REGULATION_OF_SIGNALING_BY_CBL VECCHI_GASTRIC_CANCER_EARLY_DN BROWNE_HCMV_INFECTION_48HR_UP RIZKI_TUMOR_INVASIVENESS_3D_UP ISSAEVA_MLL2_TARGETS JOHNSTONE_PARVB_TARGETS_3_UP YAMAZAKI_TCEB3_TARGETS_DN ZHU_CMV_24_HR_DN ZHENG_FOXP3_TARGETS_IN_THYMUS_UP HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP GAVIN_FOXP3_TARGETS_CLUSTER_P2 REACTOME_NEPHRIN_INTERACTIONS SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP AMIT_SERUM_RESPONSE_240_MCF10A NUTT_GBM_VS_AO_GLIOMA_UP MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 ALFANO_MYC_TARGETS EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP MARSON_FOXP3_TARGETS_STIMULATED_UP LU_TUMOR_ANGIOGENESIS_UP VERHAAK_GLIOBLASTOMA_PRONEURAL CHENG_RESPONSE_TO_NICKEL_ACETATE ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP REACTOME_MYOGENESIS MORI_LARGE_PRE_BII_LYMPHOCYTE_DN BECKER_TAMOXIFEN_RESISTANCE_DN CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN KEGG_PROTEASOME NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN REACTOME_DEVELOPMENTAL_BIOLOGY ONDER_CDH1_TARGETS_2_UP VALK_AML_CLUSTER_15 ZHAN_MULTIPLE_MYELOMA_HP_DN BIOCARTA_PROTEASOME_PATHWAY WNT_SIGNALING REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN STONER_ESOPHAGEAL_CARCINOGENESIS_UP TAVAZOIE_METASTASIS DANG_MYC_TARGETS_DN JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP LIAO_HAVE_SOX4_BINDING_SITES LEE_LIVER_CANCER_DENA_UP KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN LEE_LIVER_CANCER_ACOX1_UP CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION ULE_SPLICING_VIA_NOVA2
MPEA 0.55 0.6243 0.7273 0.6219 0.6973 0.5498 0.6250 0.576 0.5909 0.6154 0.5769 0.7674 0.5870 0.6218 0.5882 0.6471 0.7500 0.6418 0.6818 0.6250 0.5641 0.4444 0.6923 0.72 0.6245 0.6479 0.6667 0.6829 0.7308 0.5 0.6567 0.7273 0.7391 0.5451 0.6914 0.5971 0.6667 0.6393 0.5362 0.7097 0.6538 0.4545 0.7895 0.6 0.68 0.5811 0.5263 0.6064 0.5577 0.6538 0.60 0.52 0.6173 0.6285 0.7500 0.6429 0.6739 0.7083 0.6750 0.9444 0.6207 0.6216 0.7154 0.5759 0.7143 0.7179 0.6316 0.6410 0.6585 0.6346 0.6792 0.6944 0.6364 0.5730 0.7895 0.6609 0.5510 0.6099 0.6030 0.6250 0.5652 0.7922 0.6133 0.6667 0.7222 0.5484 0.6225 0.5928 0.5714 0.6627 0.6541 0.6538 0.7315 0.6013 0.7080 0.725 0.8125 0.6667 0.5625 0.650 0.500 0.5714 0.6396 0.5778 0.3684 0.6316 0.7048 0.5806 0.6333 0.625 0.6190 0.6170 0.6818 0.80 0.8889 0.6131 0.6096 0.7059 0.6818 0.8462 0.6935 0.7674 0.5882 0.6364 0.5970 0.6429 0.7500 0.55 0.6964 0.5128 0.6471 0.5778 0.5631 0.6154 0.5714
GSEA 0.40 0.4682 0.6364 0.4925 0.6122 0.4645 0.4674 0.448 0.4091 0.4615 0.4423 0.6279 0.4348 0.4958 0.3529 0.5294 0.4167 0.4955 0.5455 0.4375 0.5385 0.2963 0.6154 0.48 0.5217 0.5211 0.5897 0.5203 0.5769 0.5 0.4925 0.4545 0.5652 0.4549 0.6235 0.4532 0.4667 0.4918 0.4348 0.5806 0.5769 0.3636 0.6842 0.6 0.56 0.4717 0.4737 0.4787 0.4615 0.7308 0.55 0.38 0.5556 0.5217 0.5625 0.5357 0.5000 0.5417 0.5958 0.7222 0.5517 0.4595 0.6231 0.4643 0.5238 0.6410 0.5789 0.5385 0.5122 0.5385 0.5094 0.5000 0.5758 0.5056 0.7368 0.5460 0.4558 0.4709 0.5427 0.5312 0.5000 0.6753 0.4533 0.5714 0.7222 0.3978 0.4768 0.5090 0.3673 0.5754 0.5639 0.5385 0.6296 0.4695 0.5752 0.650 0.7500 0.5556 0.3750 0.575 0.425 0.4694 0.5635 0.4444 0.3158 0.4737 0.5619 0.5806 0.6667 0.500 0.6429 0.4681 0.5000 0.75 0.6111 0.4599 0.4813 0.7059 0.6364 0.7692 0.6452 0.6977 0.5294 0.5455 0.4179 0.5714 0.6944 0.45 0.6250 0.4872 0.4510 0.4667 0.4854 0.4872 0.4286 
# t.test(enrichment_ratio_dcor,enrichment_ratio_ttest)
enrichment_ratios_percenages <- rbind(sum(enrichment_ratio_dcor>enrichment_ratio_ttest)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor<enrichment_ratio_ttest)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor==enrichment_ratio_ttest)/length(enrichment_ratio_dcor))*100
rownames(enrichment_ratios_percenages) <- c ( "More univariate enrichment detected in Dcor", "More univariate enrichment detected in T-test", "Draw" )
colnames(enrichment_ratios_percenages) <- "Percentage"

enrichment_ratios_percenages%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
Percentage
More univariate enrichment detected in Dcor 94.0741
More univariate enrichment detected in T-test 2.2222
Draw 3.7037

Univariate Significance analysis on single pathway gene by gene Significant in GSEA and not in MPEA

enrichment_ratio_dcor <- NULL
enrichment_ratio_ttest <- NULL
for ( ii in 1:length(Significant_in_GSEA_not_in_dcor) ){
aux_genes <- intersect(pathway_collapsed[[Significant_in_GSEA_not_in_dcor[[ii]]]],colnames(expressions))
if ( identical(aux_genes, character(0))) next
aux_pathway_dcor <- dcor.test(dist(expressions[,aux_genes]),dist(genotypes),R=10000)
aux_individual_genes_in_pathway_dcor <- sapply(aux_genes,function(x) dcor.test(dist(expressions[,x]),dist(genotypes),R=10000)$p.value<0.05 )
aux_enrichment_ratio_dcor <- sum(aux_individual_genes_in_pathway_dcor)/length(aux_individual_genes_in_pathway_dcor)
enrichment_ratio_dcor[ii] <- aux_enrichment_ratio_dcor

aux_individual_genes_in_pathway_ttest <- sapply(aux_genes,function(x) t.test(expressions[,x]~genotypes)$p.value<0.05 )
aux_enrichment_ratio_ttest <- sum(aux_individual_genes_in_pathway_ttest)/length(aux_individual_genes_in_pathway_ttest)
aux_enrichment_ratio_ttest
enrichment_ratio_ttest[ii] <-aux_enrichment_ratio_ttest
}


enrichment_ratio_comparison <- rbind(enrichment_ratio_dcor,enrichment_ratio_ttest)
rownames(enrichment_ratio_comparison) <- c("MPEA","GSEA")
colnames(enrichment_ratio_comparison) <- Significant_in_GSEA_not_in_dcor

enrichment_ratio_comparison%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN PUJANA_BRCA2_PCC_NETWORK KEGG_BASE_EXCISION_REPAIR REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES REACTOME_CELL_CYCLE GARY_CD5_TARGETS_DN MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6 DAZARD_RESPONSE_TO_UV_NHEK_DN BENPORATH_PROLIFERATION NUYTTEN_EZH2_TARGETS_DN KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP RAMALHO_STEMNESS_UP DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER REACTOME_CELL_CYCLE_CHECKPOINTS REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION GENTILE_UV_RESPONSE_CLUSTER_D8 MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP REACTOME_HIV_LIFE_CYCLE FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP REACTOME_HIV_INFECTION REACTOME_CHROMOSOME_MAINTENANCE FIGUEROA_AML_METHYLATION_CLUSTER_1_DN ZHANG_BREAST_CANCER_PROGENITORS_UP PYEON_HPV_POSITIVE_TUMORS_UP MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP MARSON_BOUND_BY_E2F4_UNSTIMULATED SHEN_SMARCA2_TARGETS_UP GRADE_METASTASIS_DN REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY REACTOME_BASE_EXCISION_REPAIR REACTOME_CELL_CYCLE_MITOTIC REACTOME_TRANSCRIPTION KAUFFMANN_DNA_REPAIR_GENES ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP MITSIADES_RESPONSE_TO_APLIDIN_DN REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS BOYLAN_MULTIPLE_MYELOMA_C_D_UP FEVR_CTNNB1_TARGETS_DN REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY REACTOME_TELOMERE_MAINTENANCE BIDUS_METASTASIS_UP ZHANG_TLX_TARGETS_36HR_DN MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL KIM_WT1_TARGETS_DN MORI_PLASMA_CELL_DN ENK_UV_RESPONSE_KERATINOCYTE_DN ZHAN_EARLY_DIFFERENTIATION_GENES_DN REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP MATTIOLI_MGUS_VS_PCL ABRAMSON_INTERACT_WITH_AIRE ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP VILLANUEVA_LIVER_CANCER_KRT19_UP REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE KEGG_SPLICEOSOME MORI_MATURE_B_LYMPHOCYTE_DN DITTMER_PTHLH_TARGETS_DN CAIRO_HEPATOBLASTOMA_UP BIOCARTA_BCR_PATHWAY REACTOME_MRNA_PROCESSING HAMAI_APOPTOSIS_VIA_TRAIL_UP ROSS_AML_WITH_AML1_ETO_FUSION REACTOME_GLUCOSE_TRANSPORT REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE PECE_MAMMARY_STEM_CELL_DN DAZARD_UV_RESPONSE_CLUSTER_G6 GENTILE_UV_RESPONSE_CLUSTER_D4 REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE KAMMINGA_EZH2_TARGETS JOHNSTONE_PARVB_TARGETS_3_DN HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2 BROWNE_HCMV_INFECTION_10HR_DN PEART_HDAC_PROLIFERATION_CLUSTER_UP PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE GALE_APL_WITH_FLT3_MUTATED_UP REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC BIOCARTA_CARM_ER_PATHWAY REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION VALK_AML_CLUSTER_10 MILI_PSEUDOPODIA_HAPTOTAXIS_UP HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP BIOCARTA_PAR1_PATHWAY SESTO_RESPONSE_TO_UV_C2 CARD_MIR302A_TARGETS REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1 REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION ELLWOOD_MYC_TARGETS_DN BENPORATH_SOX2_TARGETS KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS BROWNE_HCMV_INFECTION_4HR_DN PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP WAKASUGI_HAVE_ZNF143_BINDING_SITES KIM_ALL_DISORDERS_CALB1_CORR_UP ROESSLER_LIVER_CANCER_METASTASIS_DN REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION BENPORATH_ES_1 PID_EPHA2_FWD_PATHWAY REACTOME_RNA_POL_I_TRANSCRIPTION YANG_BREAST_CANCER_ESR1_DN REACTOME_MEIOSIS REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC BOYLAN_MULTIPLE_MYELOMA_C_UP KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT HOLLMANN_APOPTOSIS_VIA_CD40_UP WHITFIELD_CELL_CYCLE_G2_M BRUINS_UVC_RESPONSE_MIDDLE PID_P38_MK2_PATHWAY KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP CHENG_IMPRINTED_BY_ESTRADIOL GAZIN_EPIGENETIC_SILENCING_BY_KRAS RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP TIEN_INTESTINE_PROBIOTICS_2HR_DN ZUCCHI_METASTASIS_UP PID_P53_REGULATION_PATHWAY BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS KIM_GERMINAL_CENTER_T_HELPER_UP PID_PS1_PATHWAY OUILLETTE_CLL_13Q14_DELETION_UP THUM_SYSTOLIC_HEART_FAILURE_DN REACTOME_APOPTOSIS PID_AR_NONGENOMIC_PATHWAY ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP JI_RESPONSE_TO_FSH_UP BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP SIG_CHEMOTAXIS BRUINS_UVC_RESPONSE_EARLY_LATE LIN_MELANOMA_COPY_NUMBER_DN REACTOME_ADAPTIVE_IMMUNE_SYSTEM JOHNSTONE_PARVB_TARGETS_2_DN ACEVEDO_LIVER_CANCER_UP KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP LAIHO_COLORECTAL_CANCER_SERRATED_DN PID_HEDGEHOG_GLI_PATHWAY LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q LIN_MELANOMA_COPY_NUMBER_UP DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP BIOCARTA_TFF_PATHWAY HOSHIDA_LIVER_CANCER_SUBCLASS_S2 BENPORATH_OCT4_TARGETS GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP GEORGES_TARGETS_OF_MIR192_AND_MIR215 KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN BILD_E2F3_ONCOGENIC_SIGNATURE LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN WOOD_EBV_EBNA1_TARGETS_DN BENPORATH_NANOG_TARGETS WINTER_HYPOXIA_DN IKEDA_MIR30_TARGETS_UP REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD HASLINGER_B_CLL_WITH_6Q21_DELETION BIOCARTA_WNT_PATHWAY YAGI_AML_WITH_T_9_11_TRANSLOCATION HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN BIOCARTA_CXCR4_PATHWAY TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN ZHAN_MULTIPLE_MYELOMA_HP_UP REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP ONKEN_UVEAL_MELANOMA_UP BILBAN_B_CLL_LPL_UP CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS KEGG_NOTCH_SIGNALING_PATHWAY HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP LEE_CALORIE_RESTRICTION_MUSCLE_DN KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS KATSANOU_ELAVL1_TARGETS_DN GYORFFY_MITOXANTRONE_RESISTANCE MULLIGHAN_NPM1_SIGNATURE_3_DN JIANG_TIP30_TARGETS_UP REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 HOFMANN_CELL_LYMPHOMA_UP STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP ABBUD_LIF_SIGNALING_1_UP DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS CHEOK_RESPONSE_TO_HD_MTX_UP REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS VERHAAK_AML_WITH_NPM1_MUTATED_UP PID_INTEGRIN_CS_PATHWAY PID_UPA_UPAR_PATHWAY REACTOME_COLLAGEN_FORMATION DALESSIO_TSA_RESPONSE GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 BIOCARTA_DC_PATHWAY NAKAJIMA_MAST_CELL REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE KIM_ALL_DISORDERS_CALB1_CORR_DN GOLUB_ALL_VS_AML_DN PID_INTEGRIN2_PATHWAY HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS KRIEG_HYPOXIA_VIA_KDM3A PID_SYNDECAN_1_PATHWAY PARK_APL_PATHOGENESIS_DN HWANG_PROSTATE_CANCER_MARKERS ALONSO_METASTASIS_NEURAL_UP AMIT_EGF_RESPONSE_120_MCF10A LI_CISPLATIN_RESISTANCE_DN REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL VERRECCHIA_RESPONSE_TO_TGFB1_C2 GROSS_ELK3_TARGETS_DN ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION NABA_COLLAGENS GHANDHI_BYSTANDER_IRRADIATION_UP KOHOUTEK_CCNT1_TARGETS TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN KOBAYASHI_EGFR_SIGNALING_6HR_DN REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP KEGG_ARACHIDONIC_ACID_METABOLISM KANG_AR_TARGETS_UP ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP HOLLERN_MICROACINAR_BREAST_TUMOR_UP WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN MIKKELSEN_MEF_ICP_WITH_H3K27ME3 GHANDHI_DIRECT_IRRADIATION_UP BIOCARTA_CYTOKINE_PATHWAY MIKKELSEN_MEF_LCP_WITH_H3K27ME3 YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP VERRECCHIA_RESPONSE_TO_TGFB1_C1 PID_RXR_VDR_PATHWAY XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES HUPER_BREAST_BASAL_VS_LUMINAL_UP NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN JEON_SMAD6_TARGETS_UP PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP PID_INTEGRIN5_PATHWAY BIOCARTA_STEM_PATHWAY NAKAMURA_ADIPOGENESIS_EARLY_UP BIOCARTA_INFLAM_PATHWAY BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS KHETCHOUMIAN_TRIM24_TARGETS_UP NAKAJIMA_EOSINOPHIL SEMENZA_HIF1_TARGETS MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP AMIT_EGF_RESPONSE_120_HELA YANG_MUC2_TARGETS_DUODENUM_6MO_DN FIGUEROA_AML_METHYLATION_CLUSTER_5_DN REACTOME_AMINE_LIGAND_BINDING_RECEPTORS SABATES_COLORECTAL_ADENOMA_UP PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A MADAN_DPPA4_TARGETS URS_ADIPOCYTE_DIFFERENTIATION_UP ONDER_CDH1_SIGNALING_VIA_CTNNB1 KERLEY_RESPONSE_TO_CISPLATIN_UP CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN MARKEY_RB1_CHRONIC_LOF_DN SHEN_SMARCA2_TARGETS_DN NABA_ECM_AFFILIATED KIM_LIVER_CANCER_POOR_SURVIVAL_DN REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS MARTENS_TRETINOIN_RESPONSE_UP WATANABE_COLON_CANCER_MSI_VS_MSS_UP MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP
MPEA 0.5714 0.6316 0.7464 0.7375 0.7308 0.7021 0.7366 0.6789 0.7826 0.8114 0.7674 NA 0.6406 0.7368 0.7193 0.7227 0.8000 0.7386 0.7368 0.6970 0.6981 0.6947 NA 0.6890 0.8154 0.5238 0.7402 0.7297 0.8133 0.7701 NA 0.7982 0.6897 NA 0.7500 0.7254 0.7557 0.6815 0.5417 0.7049 0.6238 0.7407 0.68 0.6154 NA 0.7368 0.8636 0.7570 0.6932 0.6864 0.6591 0.6914 0.8333 0.7201 0.6667 0.8182 0.6743 0.6623 0.7667 0.6154 0.6883 0.6988 0.8182 0.7321 0.6949 0.6296 0.5938 0.77 NA 0.5581 0.7407 0.7963 0.8846 0.6620 0.8585 0.8605 0.7407 0.7812 0.8214 NA 0.6535 0.7111 0.5957 0.7297 0.6531 0.7742 0.7917 0.716 0.6154 0.7083 0.7266 0.7407 NA NA 0.5882 0.6512 0.6415 0.7500 0.7209 0.7727 0.60 NA 0.750 0.6863 0.5833 0.6977 NA 0.8333 0.7273 0.7556 0.8696 0.6806 0.3125 0.8000 0.5263 0.7869 0.7778 0.8095 0.6364 0.6493 0.7190 0.6154 0.6 0.7167 0.5532 NA 0.7059 0.6545 0.7241 0.6744 0.6786 0.7368 0.6154 0.6129 0.6087 0.61 0.664 0.5667 0.6824 0.6615 0.6133 0.700 0.6331 0.6786 NA 0.6829 NA 0.6889 0.6000 0.6571 0.6825 0.5676 0.6225 0.7714 0.45 0.6832 0.6536 0.7273 NA 0.6909 NA 0.5556 0.6261 NA 0.6 NA 0.5806 0.6098 0.4815 0.6250 0.7059 0.6522 0.6204 0.6232 0.5909 0.5455 0.6415 0.5306 0.6923 0.6818 0.7326 0.6486 NA 0.6522 0.7059 0.6296 0.6833 0.5814 0.5634 0.6706 0.5432 0.7692 0.6881 0.7027 0.7273 0.5887 0.6364 0.6522 0.6863 0.7500 0.6190 0.8421 0.6038 0.7820 0.72 0.6389 0.5814 0.4706 0.6957 0.6327 0.6667 0.7368 0.6316 0.6364 1 0.8750 0.5667 0.5789 0.6111 0.5714 0.6905 0.5652 NA 0.68 0.65 0.6250 0.6190 0.6667 0.6556 0.6 0.6964 0.6071 0.6222 0.5000 0.6047 0.75 0.6119 0.6000 0.6183 0.8108 NA 0.6061 0.6184 0.6111 0.7742 0.6125 0.5909 0.7368 0.6087 0.6667 0.6875 0.6667 0.7 0.625 0.6471 0.6098 0.6000 0.4737 0.8182 0.7059 NA 0.6444 0.5926 0.5000 0.6667 0.5610 0.7083 0.5806 0.7091 0.6875 NA 0.5652 0.7143 0.6104 0.5685 0.65 0.5294 0.7018 0.6316 0.6364 0.7917 0.6258 0.5802 0.6897 0.6575 0.6442 0.5270 0.5882 0.6102 NA 0.6111 0.6492
GSEA 0.5357 0.6316 0.6599 0.6844 0.6923 0.6809 0.6831 0.5826 0.6957 0.7105 0.7558 NA 0.6094 0.7368 0.6316 0.5798 0.6364 0.6932 0.5877 0.6061 0.5849 0.6105 NA 0.6037 0.7538 0.4762 0.6716 0.6757 0.7067 0.7356 NA 0.6906 0.6207 NA 0.6875 0.6580 0.6641 0.5924 0.3750 0.6066 0.6139 0.6728 0.62 0.5385 NA 0.7368 0.8182 0.7196 0.6250 0.6213 0.5909 0.5688 0.7778 0.6412 0.5897 0.7273 0.5486 0.5974 0.7333 0.5385 0.6364 0.6145 0.7576 0.6607 0.6271 0.5481 0.5312 0.72 NA 0.4884 0.7037 0.7037 0.8462 0.5211 0.7358 0.7907 0.7407 0.7031 0.7143 NA 0.6142 0.6222 0.5957 0.6757 0.6122 0.7097 0.7083 0.679 0.5385 0.6667 0.5899 0.7037 NA NA 0.5000 0.4884 0.5660 0.6818 0.6512 0.6818 0.55 NA 0.625 0.5686 0.5139 0.6512 NA 0.7083 0.7727 0.6889 0.7391 0.5787 0.2500 0.7333 0.3684 0.6721 0.6889 0.6667 0.4545 0.5821 0.6281 0.5128 0.5 0.6667 0.4255 NA 0.5882 0.6000 0.4138 0.6047 0.5357 0.6842 0.5385 0.6452 0.4348 0.52 0.560 0.4333 0.4941 0.5231 0.5600 0.625 0.5468 0.5357 NA 0.5793 NA 0.6444 0.5333 0.5143 0.5556 0.4865 0.5000 0.7238 0.45 0.6040 0.5556 0.7273 NA 0.5818 NA 0.4074 0.5130 NA 0.6 NA 0.5161 0.5122 0.4074 0.5625 0.6471 0.6957 0.5648 0.5362 0.5455 0.5152 0.5094 0.4490 0.6538 0.6364 0.6395 0.4595 NA 0.5217 0.5588 0.4444 0.6167 0.4651 0.4366 0.5176 0.5185 0.5000 0.5780 0.5405 0.6364 0.4762 0.5000 0.6087 0.5490 0.6875 0.5238 0.7368 0.5094 0.6992 0.68 0.4722 0.4186 0.4706 0.6087 0.4694 0.6111 0.6579 0.5263 0.5758 1 0.6667 0.5500 0.5789 0.4722 0.4524 0.6429 0.4348 NA 0.64 0.50 0.5972 0.4286 0.6667 0.5333 0.4 0.5179 0.5714 0.5333 0.4375 0.5349 0.60 0.4478 0.4333 0.4962 0.6486 NA 0.4242 0.5263 0.5556 0.6452 0.4500 0.4848 0.4737 0.3913 0.5000 0.5625 0.4583 0.6 0.375 0.5294 0.5854 0.4182 0.4211 0.5909 0.5294 NA 0.5778 0.4444 0.4444 0.5556 0.5122 0.6667 0.5484 0.5455 0.6042 NA 0.4348 0.5714 0.5065 0.4932 0.55 0.4118 0.4912 0.5614 0.5152 0.7500 0.5355 0.4444 0.5172 0.5205 0.4615 0.3649 0.4118 0.5085 NA 0.5556 0.4839 
t.test(enrichment_ratio_dcor,enrichment_ratio_ttest)
## 
##  Welch Two Sample t-test
## 
## data:  enrichment_ratio_dcor and enrichment_ratio_ttest
## t = 11.354, df = 518.55, p-value < 2.2e-16
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  0.07723829 0.10955945
## sample estimates:
## mean of x mean of y 
## 0.6730257 0.5796268
enrichment_ratios_percenages <- rbind(sum(enrichment_ratio_dcor>enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor<enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor==enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor))*100
rownames(enrichment_ratios_percenages) <- c ( "More univariate enrichment detected in Dcor", "More univariate enrichment detected in T-test", "Draw" )
colnames(enrichment_ratios_percenages) <- "Percentage"

enrichment_ratios_percenages%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
Percentage
More univariate enrichment detected in Dcor 86.6438
More univariate enrichment detected in T-test 1.0274
Draw 4.1096

Close cluster

# stopCluster(cl)

PCA plot of pathways deemed significant in MPEA but not GSEA

library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name")) 

# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "AIGNER_ZEB1_TARGETS"

## [1] "ALFANO_MYC_TARGETS"

## [1] "AMIT_SERUM_RESPONSE_240_MCF10A"

## [1] "AMIT_SERUM_RESPONSE_480_MCF10A"

## [1] "BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP"

## [1] "BAUS_TFF2_TARGETS_UP"

## [1] "BECKER_TAMOXIFEN_RESISTANCE_DN"

## [1] "BIOCARTA_PROTEASOME_PATHWAY"

## [1] "BOCHKIS_FOXA2_TARGETS"

## [1] "BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING"

## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN"

## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP"

## [1] "BROWNE_HCMV_INFECTION_48HR_UP"

## [1] "BURTON_ADIPOGENESIS_11"

## [1] "BURTON_ADIPOGENESIS_7"

## [1] "CHANG_IMMORTALIZED_BY_HPV31_UP"

## [1] "CHENG_RESPONSE_TO_NICKEL_ACETATE"

## [1] "CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN"

## [1] "CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN"

## [1] "CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY"

## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"

## [1] "DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP"

## [1] "DANG_MYC_TARGETS_DN"

## [1] "DAWSON_METHYLATED_IN_LYMPHOMA_TCL1"

## [1] "DE_YY1_TARGETS_DN"

## [1] "DELACROIX_RAR_BOUND_ES"

## [1] "DELLA_RESPONSE_TO_TSA_AND_BUTYRATE"

## [1] "DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP"

## [1] "DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN"

## [1] "EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION"

## [1] "EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP"

## [1] "FERRANDO_HOX11_NEIGHBORS"

## [1] "FUJII_YBX1_TARGETS_DN"

## [1] "GAVIN_FOXP3_TARGETS_CLUSTER_P2"

## [1] "GRADE_COLON_VS_RECTAL_CANCER_DN"

## [1] "GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN"

## [1] "GRESHOCK_CANCER_COPY_NUMBER_UP"

## [1] "HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP"

## [1] "HECKER_IFNB1_TARGETS"

## [1] "HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP"

## [1] "HOELZEL_NF1_TARGETS_DN"

## [1] "HOLLERN_EMT_BREAST_TUMOR_DN"

## [1] "HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP"

## [1] "IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN"

## [1] "INGRAM_SHH_TARGETS_DN"

## [1] "ISSAEVA_MLL2_TARGETS"

## [1] "IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM"

## [1] "JAEGER_METASTASIS_UP"

## [1] "JI_METASTASIS_REPRESSED_BY_STK11"

## [1] "JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP"

## [1] "JOHNSTONE_PARVB_TARGETS_3_UP"

## [1] "KAMMINGA_SENESCENCE"

## [1] "KEGG_PROTEASOME"

## [1] "KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3"

## [1] "KUMAR_TARGETS_OF_MLL_AF9_FUSION"

## [1] "LABBE_WNT3A_TARGETS_DN"

## [1] "LEE_LIVER_CANCER_ACOX1_UP"

## [1] "LEE_LIVER_CANCER_DENA_UP"

## [1] "LIAO_HAVE_SOX4_BINDING_SITES"

## [1] "LIU_SOX4_TARGETS_UP"

## [1] "LIU_VAV3_PROSTATE_CARCINOGENESIS_UP"

## [1] "LU_TUMOR_ANGIOGENESIS_UP"

## [1] "MAHADEVAN_IMATINIB_RESISTANCE_DN"

## [1] "MANN_RESPONSE_TO_AMIFOSTINE_UP"

## [1] "MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN"

## [1] "MARSON_FOXP3_TARGETS_STIMULATED_UP"

## [1] "MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3"

## [1] "MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN"

## [1] "MORI_LARGE_PRE_BII_LYMPHOCYTE_DN"

## [1] "NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN"

## [1] "NUTT_GBM_VS_AO_GLIOMA_UP"

## [1] "ONDER_CDH1_TARGETS_2_UP"

## [1] "ONO_AML1_TARGETS_DN"

## [1] "ONO_FOXP3_TARGETS_DN"

## [1] "PASINI_SUZ12_TARGETS_UP"

## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4"

## [1] "PENG_RAPAMYCIN_RESPONSE_UP"

## [1] "PETRETTO_CARDIAC_HYPERTROPHY"

## [1] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP"

## [1] "PLASARI_TGFB1_TARGETS_10HR_DN"

## [1] "POOLA_INVASIVE_BREAST_CANCER_UP"

## [1] "QI_PLASMACYTOMA_UP"

## [1] "REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES"

## [1] "REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS"

## [1] "REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES"

## [1] "REACTOME_DEVELOPMENTAL_BIOLOGY"

## [1] "REACTOME_G_ALPHA_I_SIGNALLING_EVENTS"

## [1] "REACTOME_L1CAM_INTERACTIONS"

## [1] "REACTOME_MYOGENESIS"

## [1] "REACTOME_NEPHRIN_INTERACTIONS"

## [1] "REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS"

## [1] "REACTOME_REGULATION_OF_SIGNALING_BY_CBL"

## [1] "REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE"

## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_DN"

## [1] "RIZKI_TUMOR_INVASIVENESS_3D_UP"

## [1] "ROME_INSULIN_TARGETS_IN_MUSCLE_DN"

## [1] "RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN"

## [1] "ROY_WOUND_BLOOD_VESSEL_DN"

## [1] "SANSOM_APC_TARGETS_DN"

## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP"

## [1] "SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY"

## [1] "SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN"

## [1] "SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP"

## [1] "SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN"

## [1] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12"

## [1] "SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5"

## [1] "SIMBULAN_PARP1_TARGETS_DN"

## [1] "SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN"

## [1] "SMID_BREAST_CANCER_NORMAL_LIKE_UP"

## [1] "SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN"

## [1] "STONER_ESOPHAGEAL_CARCINOGENESIS_UP"

## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN"

## [1] "TAVAZOIE_METASTASIS"

## [1] "TSENG_ADIPOGENIC_POTENTIAL_UP"

## [1] "ULE_SPLICING_VIA_NOVA2"

## [1] "VALK_AML_CLUSTER_15"

## [1] "VANTVEER_BREAST_CANCER_BRCA1_UP"

## [1] "VECCHI_GASTRIC_CANCER_EARLY_DN"

## [1] "VERHAAK_AML_WITH_NPM1_MUTATED_DN"

## [1] "VERHAAK_GLIOBLASTOMA_PRONEURAL"

## [1] "WIELAND_UP_BY_HBV_INFECTION"

## [1] "WNT_SIGNALING"

## [1] "WONG_IFNA2_RESISTANCE_DN"

## [1] "WOO_LIVER_CANCER_RECURRENCE_UP"

## [1] "XU_CREBBP_TARGETS_DN"

## [1] "XU_GH1_AUTOCRINE_TARGETS_UP"

## [1] "YAGI_AML_WITH_11Q23_REARRANGED"

## [1] "YAMAZAKI_TCEB3_TARGETS_DN"

## [1] "YANG_BREAST_CANCER_ESR1_LASER_DN"

## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"

## [1] "ZHAN_MULTIPLE_MYELOMA_CD2_UP"

## [1] "ZHAN_MULTIPLE_MYELOMA_HP_DN"

## [1] "ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP"

## [1] "ZHENG_FOXP3_TARGETS_IN_THYMUS_UP"

## [1] "ZHU_CMV_24_HR_DN"

PCA plot of pathways deemed significant in GSEA but not MPEA

# rownames(gsea_results_significant)
# for (name in (Significant_in_GSEA_not_in_dcor)){
#   strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
#   expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
#   genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
#   genotypes_category <- as.data.frame(genotypes_category)
#   print(name)
#   print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name")) 
#   
#   # pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
#   # biplot.pcoa(pcoa.obj)
# }